MolNFT v1 · #146582 · protein
Cryo-EM of the gmppcp-bound human dynamin-1 polymer assembled on the membrane in the constricted state
6DLU: “Cryo-EM of the gmppcp-bound human dynamin-1 polymer assembled on the membrane in the constricted state”. Electron microscopy, 2 ligands (GCP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #146582 on GenesisL1: 3D structure…
- PDB
- 6DLU
- Type
- protein
- Length
- 1,481 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-1
- EC
- 3.6.5.5
- UniProt
- Q05193
- Ligands
- GCP, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dynamin-1 (EC 3.6.5.5) | protein | 734 | 45% helix, 11% strand | Q05193 |
| P | Dynamin-1 (EC 3.6.5.5) | protein | 747 | 48% helix, 10% strand | Q05193 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains B, P
- MG · Magnesium ion · metal · 2 copies · chains B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.80 | 0.89 | 52 | GCP, MG |
| 2 | 410 | 0.79 | 0.88 | 53 | GCP, MG |
| 3 | 141 | 0.77 | 0.95 | 34 | empty |
| 4 | 199 | 0.70 | 0.86 | 26 | empty |
| 5 | 202 | 0.68 | 0.85 | 33 | empty |
Interfaces
1 interface between chains.
- B–P · 1456 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6DLU · Cryo-EM of the GMPPCP-bound human dynamin-1 polymer assembled on the membrane in the… · the same entry in another collection · chain B against B, TM-score 1.00
- Q05193 · AlphaFold monomer V2.0 prediction for dynamin-1 (Q05193) · a predicted model of the same protein · chain B against A, TM-score 0.54
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q05193
- Elsewhere: RCSB PDB 6DLU · PDBe 6DLU · UniProt Q05193
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